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- PDB-3pwp: The complex between TCR A6 and human Class I MHC HLA-A2 with the ... -

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Basic information

Entry
Database: PDB / ID: 3pwp
TitleThe complex between TCR A6 and human Class I MHC HLA-A2 with the bound HuD peptide
Components
  • A6 TCR alpha chain
  • A6 TCR beta chain
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • HuD peptide
KeywordsPROTEIN BINDING / Tax peptide / HuD epitope / nonapeptide / MHC class I / HLA-A2 / TCR A6 / cross-reactivity
Function / homology
Function and homology information


alpha-beta T cell receptor complex / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / Translocation of ZAP-70 to Immunological synapse ...alpha-beta T cell receptor complex / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / alpha-beta T cell activation / protection from natural killer cell mediated cytotoxicity / Generation of second messenger molecules / Co-inhibition by PD-1 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / detection of bacterium / T cell receptor binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / response to bacterium / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / antibacterial humoral response / tertiary granule lumen / Downstream TCR signaling / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane
Similarity search - Function
T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : ...T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
T cell receptor alpha chain constant / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.69 Å
AuthorsBorbulevych, O.Y. / Baker, B.M.
CitationJournal: J.Immunol. / Year: 2011
Title: Conformational Melding Permits a Conserved Binding Geometry in TCR Recognition of Foreign and Self Molecular Mimics.
Authors: Borbulevych, O.Y. / Piepenbrink, K.H. / Baker, B.M.
History
DepositionDec 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: HuD peptide
D: A6 TCR alpha chain
E: A6 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,96913
Polymers94,2285
Non-polymers7418
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12520 Å2
ΔGint-66 kcal/mol
Surface area38430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)224.006, 49.065, 93.711
Angle α, β, γ (deg.)90.000, 90.070, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 4 types, 4 molecules ABDE

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


Mass: 31854.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769
#4: Protein A6 TCR alpha chain


Mass: 22088.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01848*PLUS
#5: Protein A6 TCR beta chain


Mass: 27361.365 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide HuD peptide


Mass: 1045.189 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 74 molecules

#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG3350, 0.1M TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å
DetectorDetector: CCD
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.69→20 Å / Num. all: 28642 / Num. obs: 27038 / % possible obs: 94.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 61.8 Å2 / Rmerge(I) obs: 0.078 / Χ2: 1.165 / Net I/σ(I): 17
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.69-2.752.70.379100.78263.2
2.75-2.82.80.34210140.872.3
2.8-2.8530.33511370.78979.6
2.85-2.913.20.31712060.86285.6
2.91-2.973.30.29812960.8592.7
2.97-3.043.50.2813790.87495.7
3.04-3.123.70.22314140.90699.6
3.12-3.23.80.18814050.967100
3.2-3.293.80.16414440.979100
3.29-3.43.80.12913980.98899.9
3.4-3.523.80.11514301.17699.9
3.52-3.663.80.09914191.169100
3.66-3.833.80.08814431.551100
3.83-4.033.80.07913991.49199.9
4.03-4.283.80.06214601.44899.5
4.28-4.63.80.05514251.75199.4
4.6-5.063.70.0514401.62399.9
5.06-5.773.80.04814481.423100
5.77-7.223.70.04814651.17599.7
7.22-203.50.03915060.84399.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å19.83 Å
Translation3.5 Å19.83 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
SGX-CATdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AO7

1ao7


Resolution: 2.69→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.897 / WRfactor Rfree: 0.2459 / WRfactor Rwork: 0.1899 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8324 / SU B: 25.665 / SU ML: 0.254 / SU Rfree: 0.3735 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.371 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2587 1371 5.1 %RANDOM, 5%
Rwork0.1979 ---
all0.2009 28702 --
obs0.2009 27035 94.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.93 Å2 / Biso mean: 55.0952 Å2 / Biso min: 33.67 Å2
Baniso -1Baniso -2Baniso -3
1--4.17 Å20 Å21.27 Å2
2--5 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 2.69→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6638 0 47 66 6751
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0216867
X-RAY DIFFRACTIONr_angle_refined_deg1.691.9359324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6115826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9223.903351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.336151088
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4651548
X-RAY DIFFRACTIONr_chiral_restr0.1210.2968
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025369
X-RAY DIFFRACTIONr_nbd_refined0.1310.082637
X-RAY DIFFRACTIONr_nbtor_refined0.3230.54479
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.5396
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1080.0853
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2690.58
X-RAY DIFFRACTIONr_mcbond_it0.94324212
X-RAY DIFFRACTIONr_mcangle_it1.58836680
X-RAY DIFFRACTIONr_scbond_it0.87423042
X-RAY DIFFRACTIONr_scangle_it1.432643
LS refinement shellResolution: 2.69→2.76 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 66 -
Rwork0.283 1230 -
all-1296 -
obs--62.58 %

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